Sorry, I should have made it clearer. I have a test suite for some libraries and it runs all fine and dandy. In order to get code coverage, I simply added use Devel::Cover to the test program which causes the warning to be thrown. The output from Devel::Cover is still created in cover_db, and I can run the cover command to get pretty output and that all works just fine.
So, in short, everything is installed and working, I'm just confused why that warning is being thrown. I did find while searching yesterday that it the 'blib' thing might have something to do with an autoloader and indeed, Devel::Cover makes use of DynaLoader.